Manual of Environmental Microbiology, Third Edition

I. Introduction to Environmental Microbiology

Introduction to Environmental Microbiology
Neighborhoods and Community Involvement: No Microbe Is an Island
Prokaryotic Diversity: Form, Ecophysiology, and Habitat

II. General Methodology

Overview: General Methodology
Analytical Imaging and Microscopy Techniques
Cultivation of Bacteria and Fungi
Cultivation of Algae and Protozoa
Cultivation and Assay of Animal Viruses
Cultivation of Microbial Consortia and Communities
Lipid Analyses for Viable Microbial Biomass, Community Composition, Metabolic Status, and In Situ Metabolism
Physiological Profiling of Microbial Communities
Molecular Approaches for the Measurement of Density, Diversity, and Phylogeny
Phylogenetic and Genomic Analysis
Bioreporters, Biosensors, and Microprobes
Ecology at Long-Term Research Sites: Integrating Microbes and Ecosystems
Quality Assurance
Issues of Study Design and Statistical Analysis for Environmental Microbiology

III. Water Microbiology in Public Health

Overview of Water Microbiology as It Relates to Public Health
Waterborne Transmission of Infectious Agents
Detection of Microorganisms in Environmental Freshwaters and Drinking Waters
Detection of Protozoan Parasites in Source and Finished Drinking Water
Microbial Indicators of Marine Recreational Water Quality
Detection of Viruses in Environmental Waters, Sewage, and Sewage Sludges
Detection of Bacterial Pathogens in Wastewater and Sludge
Detection of Pathogenic Bacteria, Viruses, and Parasitic Protozoa in Shellfish
Control of Microorganisms in Source Water and Drinking Water
Assessing the Efficiency of Wastewater Treatment
Modeling the Fate of Microorganisms in Water, Wastewater, and Soil
Estimating the Risk of Infectious Disease Associated with Pathogens in Drinking Water
Toxic Photosynthetic Microbes

IV. Aquatic Environments

An Overview of Methodologies in Aquatic Microbial Ecology
Cultivating Microorganisms from Dilute Aquatic Environments:
      Melding Traditional Methodology with New Cultivation
Techniques and Molecular Methods
Primary Productivity and Producers
Bacterial Secondary Productivity
Community Structure: Bacteria and Archaea
Viral Community Structure
Protistan Community Structure
Decomposition and Fungal Community Structure in Aquatic Environments
Bacterial Organic Carbon Cycling in Aquatic Environments
Environmental Genomics of C1 Metabolism
Sulfur Cycling
Nitrogen Cycling in Aquatic Environments
The Marine Phosphorus Cycle
Microbial Metal Cycling in Aquatic Environments
Biofilms on Living Surfaces
Extreme High-Pressure Marine Environments

V. Soil, Rhizosphere, and Phyllosphere

Introduction and Overview: Soil, Rhizosphere, and Phyllosphere
Surface Soil Microbial Sampling Methods
Application of Phylogenetic Techniques in Studies of Soil Microbial Communities
Sampling Viruses from Soil
Isolation, Culture, and Detection of Arbuscular Mycorrhizal Fungi
Isolation, In Planta Detection, and Uses of Endophytic Bacteria for Plant Protection
Methods of Soil Microbial Community Analysis
Microarrays: Design and Use for Agricultural and Environmental Applications
PCR: Agricultural and Environmental Applications for Soil Microbes
Quantification of Nitrogen Transformations
Quantifying the Metabolic Activity of Soil- and Plant-Associated Microbes
Soil Enzymes: Linking Proteomics and Ecological Processes
Use of Immunofluorescence Microscopy and Fluorescence In Situ
     Hybridization Combined with CMEIAS and Other Image Analysis
Tools To Study the Autecology of Soil- and Plant-Associated Microbes
Reporter Gene Systems Useful in Evaluating In Situ Gene Expression by Soil- and Plant-Associated Bacteria
Identifying Microorganisms Involved in Specific In Situ Functions: Experimental 
     Design Considerations for rRNA Gene-Based Population Studies and Sequence-
     Selective PCR Assays
Mobile Gene Elements in Environmental Microbial Communities
Microorganisms Associated with Soil Arthropods
Lipid Fingerprinting of Soil Microbial Communities

VI. Subsurface and Landfills

Overview of Issues in Subsurface and Landfill Microbiology
Drilling, Coring, and Sampling Subsurface Environments
Anaerobic Decomposition of Refuse in Landfills and Methane Oxidation in Landfill Covers
Biogeochemistry of Aquifer Systems
Determining the Terminal Electron-Accepting Reaction in the Saturated Subsurface
Transport of Microorganisms in the Terrestrial Subsurface: In Situ and Laboratory Methods
Oil Field Microbiology
Placement of Drinking Water Wells and Their Protection

VII. Aerobiology

Introduction to Aerobiology
Sampling for Airborne Microorganisms
Analysis of Bioaerosol Samples
Fate and Transport of Microorganisms in Air
Airborne Fungi and Mycotoxins
Airborne Bacteria and Endotoxin
Legionellae and Legionnaires’ Disease
Airborne Viruses
Aerobiology of Agricultural Pathogens

VIII. Biotransformation and Biodegradation

Overview: Biotransformation and Biodegradation
Functional Gene Arrays for Microbial Community Analysis
Methods for Soil Metagenomics: Extraction and Cloning of Soil DNA
Using Genetic Algorithms To Optimize Functions of Microbial Ecosystems
Metagenomic Methods for the Identification of Active Microorganisms and Genes in Biodegradation Processes
Proteomic Analysis of Extracellular Enzymes Produced by Wood-Degrading Fungi
Current Progress in the Application of Mycoremediation to Soil Cleanup
Fungal Solid-State Fermentation Systems for Bioconversion of Lignocellulosic Biomass:
     Process Protocol and Applications
Characterization of Microeukaryota in Natural Environments
Methods Useful in Assessing Biological and Chemical Activity of
     Low-Molecular-Weight Brown Rot Fungal Metabolites
Techniques for Studying Uncultured and Cultured Magnetotactic Bacteria
Growth of Electrode-Reducing Bacteria
Microbially Mediated Anaerobic Iron (II) Oxidation at Circumneutral pH
Isolation, Enumeration, Growth, and Preservation of Acidophilic Prokaryotes
Molecular Techniques for the Study of Toxic Metal Resistance Mechanisms in Bacteria
Synchrotron-Based Techniques for Monitoring Metal Transformations
Techniques for Studying Microbial Transformations of Metals and Radionuclides
Arsenate-Respiring Bacteria
Biotransformations of Manganese
Microbial Fe (III) Reduction: Ecological and Physiological Considerations